def remove_projection_direction(self, coords, prev_point):
prev_point = np.copy(prev_point)
rot_matrix = euler_matrix(self.M[0], self.M[1], self.M[2], 'szyx')
prev_point_rot = np.dot(rot_matrix, np.hstack([prev_point, 1]))
new_point = np.dot(rot_matrix, np.hstack([coords, 1]))
new_point[0] = prev_point_rot[0]
coords = np.dot(np.linalg.inv(rot_matrix), new_point)
return coords
def compute_matrix(self):
""" Compute rotation matrix to align Z axis to this vector. """
if abs(self.vector[0]) < 0.00001 and abs(self.vector[1]) < 0.00001:
rot = math.radians(0.00)
tilt = math.radians(0.00)
else:
rot = math.atan2(self.vector[1], self.vector[0])
tilt = math.acos(self.vector[2])
psi = 0
self.matrix = euler_matrix(-rot, -tilt, -psi, 'szyz')
def matrixFromGeometry(shifts, angles, inverseTransform):
""" Create the transformation matrix from a given
2D shifts in X and Y...and the 3 euler angles.
"""
radAngles = -np.deg2rad(angles)
M = tfs.euler_matrix(radAngles[0], radAngles[1], radAngles[2], 'szyz')
if inverseTransform:
M[:3, 3] = -shifts[:3]
M = np.linalg.inv(M)
else:
M[:3, 3] = shifts[:3]
return M
def matrixFromGeometry(shifts, angles):
""" Create the transformation matrix from given
2D shifts in X and Y and the 3 euler angles.
:param shifts: input list of shifts
:param angles: input list of angles
:return matrix
"""
radAngles = -np.deg2rad(angles)
M = transformations.euler_matrix(radAngles[0], radAngles[1], radAngles[2],
'szyz')
M[:3, 3] = -shifts[:3]
M = np.linalg.inv(M)
return M
def __setParticleTransform2D(self, particle, row):
angles = self._angles
shifts = self._shifts
ips = self._invPixelSize
def _get(label):
return float(getattr(row, label, 0.))
shifts[0] = _get('rlnOriginX') * ips
shifts[1] = _get('rlnOriginY') * ips
angles[2] = -_get('rlnAnglePsi')
radAngles = -np.deg2rad(angles)
M = tfs.euler_matrix(radAngles[0], radAngles[1], radAngles[2], 'szyz')
M[:3, 3] = shifts[:3]
particle.getTransform().setMatrix(M)
def matrixFromGeometry(shifts, angles, inverseTransform):
""" Create the transformation matrix from a given
2D shifts in X and Y...and the 3 euler angles.
"""
from pwem.convert.transformations import euler_matrix
from numpy import deg2rad
radAngles = -deg2rad(angles)
M = euler_matrix(radAngles[0], radAngles[1], radAngles[2], 'szyz')
if inverseTransform:
from numpy.linalg import inv
M[:3, 3] = -shifts[:3]
M = inv(M)
else:
M[:3, 3] = shifts[:3]
return M
def _getTransformMatrix(row, invert):
shiftx = row.get(SHIFTX, 0)
shifty = row.get(SHIFTY, 0)
shiftz = row.get(SHIFTZ, 0)
tilt = row.get(TILT, 0)
psi = row.get(PSI, 0)
rot = row.get(ROT, 0)
shifts = (float(shiftx), float(shifty), float(shiftz))
angles = (float(rot), float(tilt), float(psi))
radAngles = -np.deg2rad(angles)
M = tfs.euler_matrix(radAngles[0], radAngles[1], radAngles[2], 'szyz')
if invert:
M[0, 3] = -shifts[0]
M[1, 3] = -shifts[1]
M[2, 3] = -shifts[2]
M = np.linalg.inv(M)
else:
M[0, 3] = shifts[0]
M[1, 3] = shifts[1]
M[2, 3] = shifts[2]
return M
def __setParticleTransformProj(self, particle, row):
angles = self._angles
shifts = self._shifts
ips = self._invPixelSize
def _get(label):
return float(getattr(row, label, 0.))
shifts[0] = _get('rlnOriginX') * ips
shifts[1] = _get('rlnOriginY') * ips
shifts[2] = _get('rlnOriginZ') * ips
angles[0] = _get('rlnAngleRot')
angles[1] = _get('rlnAngleTilt')
angles[2] = _get('rlnAnglePsi')
radAngles = -np.deg2rad(angles)
# TODO: jmrt: Maybe we should test performance and consider if keeping
# TODO: the matrix and not creating one everytime will make things faster
M = tfs.euler_matrix(radAngles[0], radAngles[1], radAngles[2], 'szyz')
M[:3, 3] = -shifts[:3]
M = np.linalg.inv(M)
particle.getTransform().setMatrix(M)
def createPhantomsStep(self):
mwfilter = self.mwfilter.get()
rotmin = self.rotmin.get()
rotmax = self.rotmax.get()
tiltmin = self.tiltmin.get()
tiltmax = self.tiltmax.get()
psimin = self.psimin.get()
psimax = self.psimax.get()
fnVol = self._getExtraPath("phantom000.vol")
if self.option.get() == 0:
inputVol = self.inputVolume.get()
fnInVol = inputVol.getLocation()[1]
dim = inputVol.getDim()
if mwfilter:
mwangle = self.mwangle.get()
self.runJob(
"xmipp_transform_filter",
" --fourier wedge -%d %d 0 0 0 -i %s -o %s" %
(mwangle, mwangle, fnInVol, fnVol))
else:
self.runJob("xmipp_image_convert",
" -i %s -o %s" % (fnInVol, fnVol))
else:
desc = self.create.get()
fnDescr = self._getExtraPath("phantom.descr")
fhDescr = open(fnDescr, 'w')
fhDescr.write(desc)
fhDescr.close()
dim = [desc.split()[0], desc.split()[1], desc.split()[2]]
self.runJob("xmipp_phantom_create",
" -i %s -o %s" % (fnDescr, fnVol))
if mwfilter:
mwangle = self.mwangle.get()
self.runJob(
"xmipp_transform_filter",
" --fourier wedge -%d %d 0 0 0 -i %s -o %s" %
(mwangle, mwangle, fnVol, fnVol))
self.outputSet = self._createSetOfSubTomograms(
self._getOutputSuffix(SetOfSubTomograms))
self.outputSet.setDim(dim)
self.outputSet.setSamplingRate(self.sampling.get())
coordsBool = self.coords.get()
if coordsBool:
tomos = self.tomos.get()
tomo = tomos.getFirstItem()
tomoDim = tomo.getDim()
self.coords = self._createSetOfCoordinates3D(tomos)
subtomobase = SubTomogram()
acq = TomoAcquisition()
subtomobase.setAcquisition(acq)
subtomobase.setLocation(fnVol)
subtomobase.setSamplingRate(self.sampling.get())
transformBase = Transform()
transformBase.setMatrix(np.identity(4))
subtomobase.setTransform(transformBase)
if coordsBool:
coor = Coordinate3D()
coor.setVolume(tomo)
coor.setX(np.random.randint(0, tomoDim[0]),
const.BOTTOM_LEFT_CORNER)
coor.setY(np.random.randint(0, tomoDim[1]),
const.BOTTOM_LEFT_CORNER)
coor.setZ(np.random.randint(0, tomoDim[2]),
const.BOTTOM_LEFT_CORNER)
subtomobase.setCoordinate3D(coor)
subtomobase.setVolName(tomo.getFileName())
self.coords.append(coor)
self.coords.setBoxSize(subtomobase.getDim()[0])
self.outputSet.append(subtomobase)
for i in range(int(self.nsubtomos.get()) - 1):
fnPhantomi = self._getExtraPath("phantom%03d.vol" % int(i + 1))
rot = np.random.randint(rotmin, rotmax)
tilt = np.random.randint(tiltmin, tiltmax)
psi = np.random.randint(psimin, psimax)
self.runJob(
"xmipp_transform_geometry",
" -i %s -o %s --rotate_volume euler %d %d %d " %
(fnVol, fnPhantomi, rot, tilt, psi))
if mwfilter:
self.runJob(
"xmipp_transform_filter",
" --fourier wedge -%d %d 0 0 0 -i %s -o %s" %
(mwangle, mwangle, fnPhantomi, fnPhantomi))
subtomo = SubTomogram()
subtomo.setAcquisition(acq)
subtomo.setLocation(fnPhantomi)
subtomo.setSamplingRate(self.sampling.get())
A = euler_matrix(np.deg2rad(psi), np.deg2rad(tilt),
np.deg2rad(rot), 'szyz')
transform = Transform()
transform.setMatrix(A)
subtomo.setTransform(transform)
if coordsBool:
coor = Coordinate3D()
coor.setVolume(tomo)
coor.setX(np.random.randint(0, tomoDim[0]),
const.BOTTOM_LEFT_CORNER)
coor.setY(np.random.randint(0, tomoDim[1]),
const.BOTTOM_LEFT_CORNER)
coor.setZ(np.random.randint(0, tomoDim[2]),
const.BOTTOM_LEFT_CORNER)
subtomo.setCoordinate3D(coor)
subtomo.setVolName(tomo.getFileName())
self.coords.append(coor)
self.outputSet.append(subtomo)
if coordsBool:
self.outputSet.setCoordinates3D(self.coords)